I used flashboot to flash the main kernel and image and rebooted into kindle 4.1.0. I think that is where the problem is, I didn't flash everything I needed to before, will try again.

FYI (as mentioned elsewhere) fastboot cannot flash the main partition, which is too big for fastboot protocol, but a FALSE "success" report is returned. That is why we must flash main using "dd" at a diags ssh command prompt (or in a script). You apparently figured this out, but it is worth clarifying here for anybody reading this thread.